This one bothers me. I don't like the idea of being unable to take inventory to zero. It simply gets in the way of shipping and therefore impedes servicing the customer. Receiving is frequently behind the 8-ball when it comes to data entry. Unfortunate but it's reality.
I suppose you could let shipping send the product but then, wait until the receiving is caught up a day or so later and then enter the invoicing.
If it's just a matter of QOH being wrong, then inventory counts are in order.
COGS on the shipment will be wrong any time the QOH goes negative, particularly in FIFO or LIFO scenarios. Average Cost may affect it but I don't remember how Sage figures out the cost to use when inventory is 0 or less. For standard cost, I seem to recall that there is no real issue there. If costs for the item don't change rapidly, it should create a huge effect on the G/L side.
In any case, this is generally considered to be more of a process problem than a software problem. Some accounting systems are set up to disallow shipping in to negative quantities but that always slows down the billing process which creates it's own laundry list of problems.
But nothing should ever get in the way of sending a shipment to a customer. Accountants will have to get used to the idea that they will have to make some adjustments, for better or worse.